


Working Things Out

by afteriwake



Series: And Now I'm Learning You [16]
Category: Doctor Who, Sherlock (TV), Star Trek: Alternate Original Series (Movies)
Genre: F/M, Gen
Language: English
Status: Completed
Published: 2014-09-30
Updated: 2014-09-30
Packaged: 2018-02-19 09:40:05
Rating: General Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,512
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2383598
Author URL: https://archiveofourown.org/users/afteriwake/pseuds/afteriwake
Summary: <blockquote class="userstuff">
              <p>Once John wakes up after he's done healing from his injuries he and Molly begin to avoid each other. But when they end up together in the same room as Amy she forces them to talk things out and come to an understanding.</p>
            </blockquote>





	Working Things Out

**Author's Note:**

> I enjoyed writing this one a lot, not just because Molly gets to stand up for herself but also because it really does solve a few problems that might have cropped up with Sherlock and the Doctor Who characters knowing Khan really isn't Sherlock's twin. I'm quite proud of myself for my solution.

It didn't take John long to wake up. Three days after he was brought on board he was awake and healed, and only then did Sherlock leave his side. The rest of his friends were quite relieved that he was all right; Lestrade and Mrs. Hudson went to his room to check in on him and talk about everything that had happened. Molly had been invited to join them but she had declined, opting to stay in her and Khan's room instead. She was still angry at John, even all these months later, and while she was glad he was okay the less time she had to spend with him the better. But even she needed to eat sometimes, and at the moment she was in the kitchen with Amy and Khan. Amy was making lunch for herself and Rory, and she'd offered to make enough for Khan and Molly as well, and they'd taken her up on the offer. They had been chatting about unimportant things when it tapered off into a companionable silence. After a few minutes Amy spoke. “Molly, why don't you want to talk to John?” she asked.

She sighed. “Do you remember the day you, Nyota and I went out and left the men alone?”

“Yeah.” Then her eyes widened. “That was the day they all went to the pub, wasn't it?”

“Yes,” Khan replied. “I spotted John first and tried to leave without speaking to him. It didn't work out as well as I'd hoped.”

“ _That_ is an understatement,” Molly said with a wry smile. “Anyway, John called me later that day and beat around the bush about what he wanted to know, and he didn't take the news that Khan and I were not only dating but that we were living together well. He more or less said he thought my taste in men was suspect because I went out on a few dates with Moriarty.”

Amy winced. “It's a _really_ bad idea to use past relationships in an argument, even if you aren't dating the person you're arguing with.”

“Precisely,” Molly said with a nod. “And while I'm glad he's okay I'm not in the mood to deal with him. I'm not as upset, because something good did come out of all of it, but I still don't want to interact with him very much. It's very disheartening to have a mistake like that thrown in your face.”

“But Moriarty fooled everyone, yeah?” Amy asked. “I mean, not just you but John and Sherlock too.”

“Apparently that didn't count,” Molly said with another sigh. “It was just my stupid mistake that mattered.”

“Personally I'm not particularly fond of John for a comment he made regarding Molly at the pub,” Khan said, leaning back in his chair. “He implied the only reason she and I were friendly was because I look and sound like Sherlock.”

“You never told me that,” Molly said, turning to look at him with wide eyes.

“That's probably the reason he disliked me,” Khan said with a shrug. “I didn't exactly hide my contempt at that statement. Whether he meant it as an insult or not I wasn't about to let a comment like that go. It was a slight at Molly and I don't stand for that.”

“Thank you,” Molly said, getting up out of her chair and going over to him, kissing him on the cheek.

“You could give me a better kiss as thanks,” he said, pulling her closer.

“I could,” she said with a smile before leaning in and kissing him softly.

“You two are exactly like Rory and I were at that stage in our relationship,” Amy said with a chuckle.

“And still kind of are,” Molly said when she pulled away. “You two can be lovey dovey too.”

“I suppose we can be,” Amy said, smiling.

“Could you choose another term for it, though?” Khan asked with a pained look on his face.

“I _was_ going to say adorable,” Molly said with a grin. “I didn't think you'd like that term.”

“At least it's an actual word,” Khan replied. He moved his chair slightly and pulled Molly down onto his lap, and she laughed, putting her arms around his neck. “I will put up with you calling us that. But only you.”

“I can live with that,” she said.

“I'll just do it behind your back,” Amy said with a wide grin as she finished making the sandwiches they were going to eat.

“Just make sure I don't hear it,” he replied, running a hand up and down Molly's back. He was going to say more but he heard a throat clear and he saw Sherlock standing in the doorway, with John behind him. “Yes?”

“Our brother has need of you,” Sherlock said. “It's a phone call this time, not a meeting. The Doctor sent me to fetch you.”

“Very well,” Khan said with a sigh. Molly got up off of his lap and when he stood he leaned over and kissed her. “You're more than welcome to come to the console room with me,” he said when he pulled away.

“I need to deal with him eventually, I suppose,” she said quietly. She reached over for his hand and squeezed it. “Let me know if you need to leave again, all right?”

Khan nodded. “I will.” He went to the doorway. “He's in the console room, correct?” he asked Sherlock.

“Yes,” he replied.

“I'll go there by myself,” he said. Then he looked over at John. “Upset her and I will not be pleased.”

“All right,” John said quietly, nodding. With that, Khan made his way out of the kitchen, leaving the other four in the room.

Amy looked at the two men by the door and then to Molly, and finally back to Sherlock and John. “I can make John and Rory sandwiches in a minute, if you two are hungry. You can each have one of the ones I already made.”

“Thank you,” Sherlock said with a nod. John nodded as well and they came into the kitchen. They both sat at the table, though neither of them sat where Khan had been sitting. Amy brought them each a plate, and then went back for the other two. She brought Molly hers and then set her own on the table next to Molly. There was a bit of an awkward silence as the four of them ate, and after a moment Sherlock spoke. “So,” he said quietly.

“I should probably take this back to my room and eat,” Molly said, standing up.

“You don't need to go” John said. “I'll leave.” He stood up as well.

“Both of you, sit,” Amy said, glaring at John and then at Molly. After a moment's hesitation they both sat down. “Now then. All of us have to stay on the TARDIS for God knows how long and everyone needs to get along or at least not actively avoid each other. I'm not going to pretend I know you all that well, John, but I know Molly well and she doesn't deserve to feel like she has to hide out in her room all the time. And to be honest you shouldn't either.” She moved her hand towards Molly and then John and back and forth a few more times. “So work it out.”

John looked a bit sheepish at the rebuke. “Did he tell you what happened at the pub?” he asked Molly.

She nodded. “He said you basically implied the only reason I liked him was because he looked and sounded like Sherlock.”

“I meant it in jest,” he said. “He took it literally, though. And to be honest, I thought he overreacted. But he really does care about you.”

“He loves me,” Molly said. “There's a difference.”

“I didn't know that at the time. And he said acquaintance, not girlfriend. I thought you two were simply friends. And I thought he was an arse.” John looked over at her. “I thought you needed to see him for what he was. But I guess he's an okay guy after all.”

“But you didn't trust me or my judgment, John. I had known him for months at that point. I've been living with him the entire time he's been back in London. I know him much better than you or anyone else here does, even Sherlock.”

“That's actually quite true,” Sherlock said thoughtfully. “He and I are related and spent nearly half our lives together and I still don't think I know him as well as Molly does.”

“See?” Molly said. “And it was the way you went about it. We'd barely talked in months, John. Greg probably could have brought up concerns about him and I'd have been more inclined to listen because at least Greg and I talked, even if it was mostly about work. But you called me after three months of ignoring me and acted like you had every right to dictate my personal life. Throwing that jab about me dating Moriarty in didn't help.”

John winced. “I regretted that almost as soon as you hung up on me. But I thought I was doing you a favor. I thought you deserved better than him.”

“Who did you think I deserved? Someone you handpicked for me?” She looked him in the eye. “I'm a grown woman and I can date or shag or love whomever I choose. And for right now, and probably for a very long time in the future, I choose John.”

John nodded, and then sighed. “I was just so _angry_ when I dealt with him. At first I was so sure he was Sherlock. Even with the different hairstyles they looked identical. And then he spoke and I couldn't believe that he wasn't Sherlock. And then he rebuffed my offer for the pint. I thought he was an arrogant git at that point, and I didn't even consider that maybe he didn't want to hear all about Sherlock, even though he pretty much said his family didn't approve of him. I didn't even think it must be hard for him to walk around and have people assume he was Sherlock back from the dead.”

“It has been hard for him,” she said quietly. “Until recently he's avoided anything having to do with the life Sherlock left behind, and I don't blame him.”

“Did he know Sherlock wasn't really dead? I mean, before I met him?” John asked.

Molly nodded. “He was in the room while Mycroft and I had a conversation about it. Not directly talking about Sherlock, but he read between the lines and figured it out. Mycroft and I told him everything at that point.”

“That's even more of a reason not to talk to me, I suppose,” John admitted.

“That's why I distanced myself. I would have done it with Greg, too, but I have to work with him. Or had to, at any rate.”

“Had to?” John asked, confused.

“I got sacked, after the second time someone tried to kill me. Or rather, after the money was put on my head. Only once did someone _actually_ try and kill me.” She shook her head after that. “But that's not the point. I distanced myself because I saw how much it hurt you that Sherlock was gone, and I couldn't tell you I knew he wasn't dead. After a while I just didn't know if I could keep that secret when I was around you, so it was best if I wasn't around you.”

“Greg says he didn't know until a few weeks ago,” he replied.

“He figured it out and Mycroft confirmed it,” Molly said with a nod. “Mostly because the people in Moriarty's organization had let it be known that if Sherlock, John or I were killed they'd be paid a hefty sum of money. Especially if they'd killed me first, because they assumed Sherlock or John would start making mistakes.”

“My brother and I most likely would have, too,” Sherlock said. “Both of us care for Molly greatly, though in different ways.”

“So why aren't you taking care of taking down the criminal organization now?” John asked, turning to Sherlock.

“My brother has a certain skill set I don't,” Sherlock said after just a moment's hesitation. “The criminal record that Lestrade had viewed isn't exactly complete.”

“Just how dangerous is he?” John asked, his eyes wide.

“Quite dangerous,” Sherlock said. “If he was a different person he could have been very high ranked in an organization such as Moriarty's.”

“And you knew this?” he asked Molly as he turned back to her, his jaw hanging slightly.

She nodded. “I knew, and it didn't bother me. Well, it did at first, but not as much as he had thought it would. And he proved himself to me. He's never been anything but courteous and kind to me, from the start.” She took a bite of her sandwich. “He told me the truth before we began dating, so when I did fall in love with him I knew everything.”

John leaned back in his chair. “I get the feeling I misjudged the entire situation.”

“You did, but you didn't know any better, and I couldn't set you straight without betraying Sherlock's secret,” Molly said quietly. “I'm sorry I had to lie to you, but it was vital to what Sherlock was doing.”

“And I'm sorry I put you through what I put you through, if we're making apologies,” Sherlock said.

“I suppose I should apologize for thinking I knew what was best for you when you really knew what was best for you,” John said with a slight smile.

“Apology accepted,” Molly said with a nod.

“And I accept both of your apologies,” John said.

“So. Are all of you good?” Amy asked, looking at the three of them.

“Yeah, I think we're good,” Molly said with a smile, and Sherlock and John nodded.

“Good,” she said as footsteps approached the room. After a moment Khan was in the doorway. “Do you have to leave again?”

“Not for a few more hours,” he said.

“All right. Sit down and I'll make you a sandwich. Your brother and his best friend are eating the ones I made for you and Rory,” Amy said, standing up.

“I can make my own,” Khan said, eying John warily.

“We're okay with each other, John,” Molly said with a smile.

Khan nodded. “It's going to get very strange with two people named John on board,” he said.

“We can always refer to you by your nickname,” Sherlock said. “After all, when we were children you did prefer to be called Khan.”

“If our parents had allowed it I probably would have legally changed my name to that,” he said. “But perhaps it would be easier.”

“Did you pick it for Shere Khan?” John asked.

Khan shook his head. “Genghis Khan. While Sherlock preferred pirates I was fond of leading men into war when we would pretend. Sherlock gave me the nickname and it stuck.”

“I always thought Carlton was a boring name,” Sherlock said.

“Well, I always thought your name was even more boring,” Khan replied, moving towards the refrigerator.

“I don't know. Sherlock is rather unique,” Amy said as Molly suppressed a chuckle. Amy turned to her. “What's so funny?”

Sherlock sighed. “Sherlock is my middle name. My birth name is William.”

“Really?” John asked, surprised.

“William Sherlock Scott Holmes,” Sherlock said. “Khan and I despised our names so we went by other ones. I just stuck closer to my name for the one I chose to use in adulthood.”

“I thought John Smith was a bit obvious, and when Harrison was suggested I went for it,” Khan said with a shrug. “I just wanted something that wasn't at all similar to Carlton Andrew Christopher Holmes.”

“I thought I knew you so well,” John said, looking at Sherlock.

“You should know better than most that I tend to keep secrets,” he said with a shrug.

“But Sherlock Holmes is on your tombstone,” John pointed out.

“Yes, because I told Mycroft if he put my real name on my tombstone I would make his life hell. That is a threat I am more than capable of delivering on,” he replied before taking a bite of his sandwich.

“So it's best if we just call you Khan?” Amy asked.

Khan nodded. “To be honest, John Harrison isn’t a name I particularly like. So simply calling me Khan is what I would prefer.”

“Well, we'll tell everyone to do that,” Amy said with a nod.

Molly had finished her sandwich that point and smiled at Khan. “Are you really all that hungry?” she asked.

“Not particularly,” he said. “Why?”

“I was just thinking we could spend some time alone before you left again” she said.

He nodded. “I could approve of that idea.”

“I'll wash your plate for you,” Amy said as Molly stood up.

“Thank you,” she said, turning her smile to Amy before joining Khan, who had moved to the door. “We'll see you later.”

“Don't be loud,” Sherlock said.

“Don't start, _William_ ,” Khan replied as Molly chuckled. She guided Khan out of the kitchen and they stayed quiet as they walked hand in hand down the hallway. “That conversation neatly solved a lot of problems, didn't it?”

“Yes, it did,” she said with a nod. “As much as I hate lying to my friends this will make it easier. Amy, Rory and the Doctor have been calling you Khan more than John, so now if everyone knows it's your preference it won't come off as if we're talking about someone else, or lying to everyone, even if we are. And Sherlock told John you were dangerous and had a skill set he didn't, so if they talk about it with others then they won't be surprised you're doing what Sherlock was doing now.”

“I'll just have to be careful that Sherlock's friends don't see me if I'm badly injured,” he said. “It would be strange if I'm injured when I come back and then perfectly fine the next day.”

“I just wish you wouldn't get hurt at all, but I know that's not an option,” she said with a sigh.

He stopped and pulled her close to him. “There is an end in sight, though. I have been making a significant dent in Moriarty's organization. People are slowly becoming more afraid of Carlton Holmes than they are of Sherlock Holmes or they ever were of James Moriarty, and people are not as willing to force a confrontation with me, especially with the rumors I can show up anywhere even though I was somewhere else farther away mere hours before, and any injuries I might have had are miraculously healed.”

“So the fact that the Doctor jumps around is helping?” she asked.

He nodded. “As far as the world at large knows, I've only been taking care of the threats for a little over a month. Generally as soon as I'm alerted to a new threat and I'm fully healed I have the Doctor take me two hours after I left wherever else it was that I was. So it seems I've gone from Johannesburg to Moscow, for example, or New York City to Tokyo in a matter of hours, even though it might have been three days for me.”

“That's brilliant,” she said, her eyes wide.

“There are people convinced I know magic or that I sold my soul to the devil or other supernatural nonsense like that. Very few think Sherlock and I are working together because we never appear in two different places at the same time. Most people think the injuries he sustained in the alley crippled him and I'm getting revenge. But whatever it is they think, fewer people want to have a run-in with me. I am a much scarier foe than any of Moriarty's top enforcers. In fact, I've crippled most of them so they’re no longer a threat. It's lower level people now that I'm getting rid of, for the most part.”

“So it might be over soon?” she asked hopefully.

“I hope so,” he said with a nod.

“That's the best news I've heard all day,” she said with a wide smile. “I really should show you how happy that makes me.”

“Yes, I think you should,” he murmured before he leaned in to kiss her. She pressed herself close as she kissed him back, and only pulled away when it became apparent there was a good chance they might take it too far before they got back to their room. “Let's go where there's more privacy.”

“Absolutely,” she said with a nod, grabbing his hand and nearly dragging him towards their bedroom. There was a very good chance that soon this would be over and all of them would be safe. This was definitely something that greatly pleased her, and the sooner it was all over the better.


End file.
